CellMap Project Team
Using computer vision and machine learning techniques to scalably detect subcellular structures, such as organelles, in datasets generated with next-gen vEM
United States of America
Pinned Repositories
cellmap-data
Utility for loading CellMap data for machine learning training, utilizing PyTorch, TensorStore, Xarray, and PyDantic.
cellmap-models
Repository of model architectures and network weights used for CellMap segmentations.
cosem-segmentation-analysis
Code to segment and analyze COSEM predictions
dacapo
A framework for easy application of established machine learning techniques on large, multi-dimensional images.
fibsem-tools
Tools for handling FIB-SEM data and annotations
heinrich-2021a
Resources for Heinrich et al., 2021
multiresolution-mesh-creator
openorganelle
A portal for viewing FIB-SEM datasets
pydantic-zarr
Pydantic models for Zarr
schemas
Documentation of how data, metadata, and derived data are are organized for the COSEM project
CellMap Project Team's Repositories
janelia-cellmap/heinrich-2021a
Resources for Heinrich et al., 2021
janelia-cellmap/schemas
Documentation of how data, metadata, and derived data are are organized for the COSEM project
janelia-cellmap/cosem-segmentation-analysis
Code to segment and analyze COSEM predictions
janelia-cellmap/cellmap-hackathon-blog
CellMap hackathon blog
janelia-cellmap/training_setups
Reference for parameters of the different training setups
janelia-cellmap/cosem
Java tools
janelia-cellmap/Fiji_COSEM_Predictions_Evaluation
janelia-cellmap/refinements
janelia-cellmap/annotation-metadata
Metadata for annotations
janelia-cellmap/aws-opendata
Materials pursuant to our entry in the AWS Open Data program
janelia-cellmap/cellmap-api-aws
janelia-cellmap/cloudism
AWS CDK stacks for cellmap.
janelia-cellmap/converter
A tool for converting files from one format to another.
janelia-cellmap/cosem-db
Config files for setting up a database for tracking COSEM datasets
janelia-cellmap/cosem-tutorials
Tutorials, how-tos, and demonstrations.
janelia-cellmap/cosem_notebooks
Various notebooks for one-off operations
janelia-cellmap/dacapo-dashboard
janelia-cellmap/fibsem-optflow
Repository related to optical flow calculations for fibsem images
janelia-cellmap/hot-knife
janelia-cellmap/insertion_sorting_of_predictions
janelia-cellmap/jfibsem_dat
janelia-cellmap/jsonschema-form
Schematized forms
janelia-cellmap/media
Images, videos, and other media pertaining to COSEM
janelia-cellmap/n5ng
Small python proxy to serve n5 data in neuroglancer precomputed format
janelia-cellmap/neuroglancer-url-tools
Typescript objects for synthesizing URLs for the neuroglancer visualization tool.
janelia-cellmap/open-data-registry
A registry of publicly available datasets on AWS
janelia-cellmap/organelle-watershed-agglomeration
janelia-cellmap/pegboard
Data management portal
janelia-cellmap/sheetscrape
Scraping google sheets
janelia-cellmap/workflow
Raw data to segmentations